slamdunk
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t-neumann
Streamlining SLAM-seq analysis with ultra-high sensitivity
Hi, I am dealing with quant-seq data, and I was wondering if I should use "-e" or not, also can you explain the description of "-e" in the DOCS, "Deactivates...
Dear Team, I am new to SLAMseq and trying to use SLAMDUNK for the analysis of my Slamseq data. When I am running the command "alleyoop utrrates -o try/ -r...
Hello, I have a question about the ReadCount column obtained in the TCcount CSV file. I thought I would get the number of reads that were mapped by summing all...
Hi Tobias, I'm having problems with alleyoop summary. I'm using slam dunk thought docker and I have run the following commands. slamdunk all alleyoop summary This is the command: alleyoop...
Noticed that ```alleyoop utrrates``` generates an output file ```mutationrates_utr.csv```, but this file is actually in the tsv format. Converting the csv to a tsv extension fixed issues with downstream handling,...
Hi! I am interested in using DUNK for a non-SLAMseq dataset. I have RNAseq data in which I am looking for RNA editing (including hyper-editing which yields heavily edited reads)...
Dear Tobias, we ran into the question why SNP calling is running on all samples and not only on the samples were no 4SU labelling was performed. Is there any...
Hi, @t-neumann. this is another issue which relates to the previous one, [#106](https://github.com/t-neumann/slamdunk/issues/106). We have run slamdunk 3 different ways. Without multimapping, with multimapping (`-n 1 -m`), and multimapping with...
Hi, this is another issue which relates to the previous one, [#105](https://github.com/t-neumann/slamdunk/issues/105). Our `slamdunk all` call is as follows: `slamdunk all -o res -r Homo_sapiens_assembly38_ERCC92.fasta -b GSE100708_hg38_refseq_062016_ensemblv84_3UTR.bed -t 14 -c...
Hi, @t-neumann. Thanks for the amazing technology. We are currently processing some slam-seq data. We are running our fork of Slamdunk, [https://github.com/jkobject/slamdunk](https://github.com/jkobject/slamdunk,) which has been slightly modified to map paired-end...